April 27, 2018

One of the major revisions in my own mind about the demographic and historical processes of the Holocene in relation to humans has been the reality that large and dense agglomerations of agriculturalists could be marginalized by later peoples, to the point of having a smaller genetic footprint in the future than anyone might have imagined. If you had asked me ten years ago I just wouldn’t have believed that the first farmers of Europe or South Asia wouldn’t account for the vast majority of the ancestry of the contemporary populations of the region. By “first farmers” I don’t even mean migrants. At that point, I had assumed a primarily Pleistocene indigenous hypothesis for the origin of Europeans and South Asians, with farming diffusing through a mixture of a few migrants along a demographic wave of advance.

That’s not what it looks like according to ancient DNA. In Northern Europe, it seems that around half or more of the ancestry is due to the incursions of a pastoralist steppe population during the Bronze Age. In Southern Europe and South Asia, the fraction is closer to 10-25%. But even in the latter case, the fraction of steppe ancestry is far higher than I had expected.

I had assumed that the steppe migrants would contribute 1-5% of the ancestry of Europeans and South Asians and that the spread of Indo-European languages was a matter of elite transmission and emulation. Think the Hungarians, for example, as an example of what had assumed.

So what explains what really happened?

During the Mongol conquest of Northern China Genghis Khan reputedly wanted to turn the land that had been the heart of the Middle Kingdom into pasture, first by exterminating the whole population. Part of the motive was to punish the Chinese for resisting his armies, and part of it was to increase his wealth. One of his advisors, Yelu Chucai, a functionary from the Khitai people, dissuaded him from this path through appealing to his selfishness. Chinese peasants taxed on their surplus would enrich Genghis Khan far more than enlarging his herds. Rather than focus on primary production, Genghis Khan could sit atop a more complex economic system and extract rents.

Most of you at this point can see the general framework then. For thousands of years, pastoralist people of the Inner Asian steppe and forest would extract rents out of the oikoumene by threatening them with force. The reason the East Roman Empire did not face the Hunnic onslaught during the lifetime of Attila is that they paid the horde tribute. Imperial China did the same during some periods. In other instances, civilized states found in the barbarians of the steppe useful confederates. The Tang dynasty did not collapse during the 750s because of the intervention of the Uyghurs, who suppressed the rebellion of An Lushan. In 9th century Baghdad the rise of the Turks was enabled by their usefulness in court politics and distance from any given faction.

The rise of the “gunpowder empires” during the 16th century and the eventual closing of the Inner Asian frontier with the crushing of the last embers of the Oirat confederacy between the Russian and Chinese Empires in the 18th century marked the end of thousands of years of interaction between the farmland and pasture.

But this makes us ask: when did this dynamic begin? I don’t think it was primordial. It was invented and developed over time through trial and error. I believe that the initial instinct of pastoralists was to turn farmland into pasture for his herds. This was Genghis Khan’s instinct. The rude barbarian that he was he had not grown up in the extortive system which more civilized barbarians, such as the Khitai, had been habituated to.

In these situations where pastoralists expropriated the land, there wouldn’t have been an opportunity for the farmer to raise a family. Barbarian warlords throughout history have aspired to be rich by plundering from the civilized the peoples…but would the earliest generations have understood the complexity of the institutions that they would have to extract rents out of if there wasn’t a precedent?

Instead of conventional historical dynamics of predatory elites and static peasantry, a better way to understand what occurred with the incursion of steppe pastoralists during the Bronze Age might be a simple ecological model of intra-specific competition. In a pre-state society defined by clan and tribal ties, steppe elites may have seen the farmers who were earlier residents in the territories which they were expanding into as competitors rather than resources from which a life of leisure might be obtained. In other words, instead of conquest, the dynamic was of animal competition.

Of course, pre-modern societies did not have totalitarian states and deadly technology. Rapid organized genocide in a way that we would understand was unlikely to have happened. Rather, in a world on the Malthusian margin, a few generations of deprivation may have resulted in the rapid demographic extinction of whole cultures. You don’t need to kill them if they starve because they were driven off their land.

In fact, we have some precedent of this historically. The Spaniards were intent on extracting rents out of the native peoples of the New World and living a life of leisure, but in many areas disease and exploitation resulted in demographic collapse. Imagine a conquest elite as vicious as the Spaniards, but without thousands of years of precedent that conquered peoples were more useful alive rather than dead.

Addendum: The fraction of haplogroup M, which is probably derived from Pleistocene South Asians, is greater than 50% in places like Sindh. This indicates that the steppe migrations were strongly male biased in the initial generations.

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May 30, 2017

One of the most fascinating things about ancient Egypt is its continuity, and our granular and detailed knowledge of that continuity. We can thank in part the dry climate, as well as the Egyptian penchant for putting their hieroglyphs on walls and monuments (as well as graffiti!). And we can also thank the fact that both the ancient Greeks and Hebrews, Athens and Jerusalem so to speak, were deeply connected to and perceived themselves to be indebted to Egyptian civilization. Even before the translation of the Rosetta Stone and the deciphering of ancient Egyptian writing the Hebrews’ interactions with Egyptians, in particular in Exodus, mean that their memory would echo down through the millennia (the newly Christianized Irish interpolated Egyptian ancestry into their own genealogy).

The Greek relationship with Egypt was less fraught and at greater remove than the Hebrews. But the Classical period philosophers correctly perceived that Egyptian civilization was ancient, and preceded their own. Aegean-Egyptian connections were actually more longstanding than the Classical scholars knew, in Brotherhood of Kings: How International Relations Shaped the Ancient Near East, the correspondence in state archives which have been retrieved are rather clear that Minoan civilization was part of the orbit of Egypt early on. Though Egyptians never conquered the Aegean polities, mercantile and diplomatic connections were extremely old and persistent. The late Bronze Age eruption of barbarian Sea Peoples who attacked the whole civilized Near East may have been facilitated in part by the broad familiarity engendered by widespread trade networks.

The most recent book devoted to ancient Egypt I have read was Toby Wilkinson’s The Rise and Fall of Ancient Egypt. Synthesizing extensive written material with archaeology, perhaps the most impactful argument in Wikinson’s narrative was the persistence of the temple based institutions from the Old Kingdom down to the Ptolemaic era. Religious institutions carried on even with the shocks of Nubian and Libyan conquest in the post-New Kingdom period, down to Late Antiquity. The temple at Philae in southern Egypt was an active center of the traditional religion, and therefore the culture which dates to the Old Kingdom in continuous form, down to the 6th century A.D. (when it was closed by Justinian in his kulturkampf against ancient heterodoxies).

For various ideological reasons though many people are very curious about the racial characteristics of the ancient Egyptians. There are two basic extreme positions, Afrocentrists and Eurocentrists. Though I have not done a deep dive of the literature of either group, I’ve read a few books from either camp over my lifetime. In fact I believe the last time I read the “primary literature” of Afrocentrist and Eurocentrism was when I was an early teen, and it was rather strange because both groups seem to be recapitulating racial disagreements and viewpoints relevant to the American context, and projecting them back to the ancient world.

In college I stumbled upon Mary Lefkowitz’s Not Out Of Africa, a book length argument against the more sophisticated Afrocentrist views articulated in the wake of Martin Bernal’s Black Athena: The Afroasiatic Roots of Classical Civilization. Lefkowitz was a classicist, so many of her objections were exceedingly scholarly. The reality is that the best refutation of an Afrocentrist view of of ancient Egypt, which reduces to the idea that ancient Egyptians would be recognizably black African today, are the Fayum portraits. It is notable to me how similar these portraits are to modern Copts. In fact the actor Rami Malek, of Coptic background, looks strikingly like someone who stepped out of the Fayum portraits.

I have read no book length refutation of the Eurocentrist, usually Nordicist, perspective. Mostly because this is a view associated with white supremacism, and that ideology is generally attacked on normative, not positive, grounds. But the visible evidence of the Fayum portraits is a strong refutation of the Nordic model. Of course, there is the reality that we now know that the Nordic phenotype, and the genetic components which congealed into that typical of Northern Europe today, was only coming into existence when the Old Kingdom of Egypt was already a mature civilization.

Of course both Afrocentrists and Eurocentrists will reject the evidence of the Fayum portraits became they came from the Roman era, and they would argue that the demographic nature of Egyptians changed quite a bit between that period and the end of the New Kingdom. And they are not incorrect that the period between the arrival of the Romans and the fall of the New Kingdom was characterized by a great deal of change. There were Libyan dynasties, Nubian dynasties, and periods of rule by Assyrians, Persians, and Macedonians. Large colonies of Greeks, Macedonians, and Hebrews-becoming-Jews were also resident in Egypt. Especially, but not limited to, the urban areas.

Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.

Because modern people care about the Afrocentrist question, the extent of Sub-Saharan African ancestry is highlighted in this paper. I do not think this is actually the most interesting aspect. But I’ll get to that. Since this post will be read by a fair number of people I’ll talk about the relationship of ancient and modern Egyptians to (Northern) Europeans and Sub-Saharan Africans.

The figure to the left is looking at 90 ancient Egyptian mitochondrial genomes (and some modern ones in the two rightmost columns). Since mtDNA is copious it was relatively easy to extract and analyze. Haplogroup L, the red to orange shades in the bar plots, are associated without dispute with Sub-Saharan Africa. Haplogroup U6, M1 and a few others may be “back to Africa” variants of different periods (they are generally found in Afro-Asiatic groups).

What you can see is that somewhat more than half of Ethiopia’s mtDNA lineages are L, in keeping with the whole genome estimate of Sub-Saharan African ancestry in most Cushitic populations. In Egypt there is a difference over time; haplogroup L goes from low frequencies to much higher frequencies in modern periods. The ~20% fraction in the modern samples is in line with the population wide admixture one sees in modern Egyptians of Sub-Saharan admixture.

I actually recomputed the haplogroups to a finer granularity from the supplements for readers who know this stuff well. Here they are:

Haplogroup

Count

H

2

H13c1

2

H5

2

H6b

2

HV

3

HV1a’b’c

4

HV1a2a

3

HV1b2

2

HV21

2

I

5

J1d

2

J2a1a1

2

J2a2b

2

J2a2c

4

J2a2e

3

K 16T

2

K1a

2

K1a4

2

L3

2

M1a1

4

M1a1e

2

M1a1i

2

M1a2a

2

N

2

N1’5

2

N1a1a2

2

R

3

R0

2

R0a

2

R0a1

2

R0a1a

3

R0a2

3

R0a2f

2

R2’JT

2

T

3

T1a

3

T1a2

2

T1a5

4

T1a7

7

T1a8a

2

T2

3

T2c1

2

T2c1c

2

T2e

2

U

2

U1a1

2

U1a1a3

2

U3b

3

U5a

2

U6a

2

U6a2

2

U6a3

2

U7

4

U8b1a1

3

U8b1b1

2

W3a1

2

W6

2

W8

2

X

2

X1

2

X1c

2

A quick inspection of mtDNA haplogroup frequencies shows that ancient Egyptians are not typical of modern Europeans. Not that much H, and lots of T, J and K. What that does remind me of are EarlyEuropeanFarmers. These people, who brought agriculture to Europe from Anatolia contributed a large fraction of the ancestry of modern Southern Europeans, and a lesser component to Northern Europeans.

But ultimately what’s great about this paper is that they have ancient autosomal DNA. That is, genome-wide results.

They got three samples of reasonably high quality. More precisely: “Two samples from the Pre-Ptolemaic Periods (New Kingdom to Late Period) had 5.3 and 0.5% nuclear contamination and yielded 132,084 and 508,360 SNPs, respectively, and one sample from the Ptolemaic Period had 7.3% contamination and yielded 201,967 SNPs.”

You can see the three samples on this bar plot. What is interesting is that they’re all pretty similar.

What you can see here is that to a great extent ancient Egyptians were descended from a population closely related to Natufians, or Natufians themselves. This easily explains the mtDNA affinity to Neolithic farmers: Natufians and Anatolian Neolithic populations were sister populations. The f3 statistic which looks at shared drift shows an affinity of ancient Egyptians with ancient farmer populations with Near Eastern provenance, but also with modern Sardinians. This is a common pattern, as ancient groups do not have later migration waves, with the Sardinians the modern population closest to this.

You see in the bar plot that northern Levantine populations are placed between Anatolian Neolithics and Natufians, as one might expect based on their geographical position and gene flow between these two regions. Additionally, the cyan color is associated with eastern farmers from the Zagros. I’ve already talked about gene flow from this area to the Levant recently. If you compare the Bronze Age Sidon samples I think you’ll see broad affinities with these Late Period Egyptians.

The PCA gives us results consonant with the model-based clustering. If you plot the genetic variation of ancient Egyptians they’re closest to Neolithic eastern Mediterranean populations. No great surprise.

Not the modern Egyptians. Why? It’s pretty clearly because modern Egyptians are shifted toward Sub-Saharan Africans. But there is also another component: modern Egyptians have more of the cyan eastern farmer component. What could this be?

An immediate thought comes to mind. We focus a great deal on Sub-Saharan African slavery. One reason is that it is visible. Black Africans are physically distinct from most Middle Eastern populations. But Egypt was long the center of another slave trade: “white slaves” from the Caucasus. Circassians. For hundreds of years Mamluks were recruited from the Caucasus as military slaves. They eventually became the ruling class of Egypt, until their decimation in the 19th century under Muhammad Ali (who himself was an Albanian Ottoman who never learned to speak Arabic well).

As noted in the paper earlier work looking at patterns in ancestry tracts and LD decay had made it obvious that much of the admixture of Sub-Saharan ancestry in Egypt, as in much of the Middle East, is relatively recent. In particular, it dates to the Islamic period, when trade and conquest took on new dimensions in Africa and north into Central Asia. One way ethnic minorities like Assyrians and Lebanese Christians differ from their Muslim neighbors is that they have much lower fractions of Sub-Saharan African ancestry, and no East Asian component. The latter might surprise, but remember that Central Asian Turkic slaves have been prominent in Muslim armies since at least the 9th century.

But some of the Sub-Saharan ancestry in Egyptians is old. The ancient Egyptian samples have it. To have none of it would seem strange, considering the history of contact between Nubia and Egypt, dating back to the Old Kingdom. Second, there is evidence of low levels of Sub-Saharan African gene flow into Southern Europeans. How did that happen? The highest fractions are in Spain, and can there be attributed to the Moorish period. But that explanation does not hold in much of Italy, where there are a few percent of haplogroup L. This probably is due to south-to-north gene flow across the Mediterranean during the Classical period. Some of the peoples on the south shore of the Mediterranean almost certainly already had some Sub-Saharan African admixture.

Not getting into the details of it, there are ways to explicitly model gene flow into a target population from donors defined by a phylogeny. In this case the authors tested various models of gene flow from Sub-Saharan Africans and Eurasians (non-Africans) to generate allele frequency patterns we see in modern Egyptians and ancient Egyptians.

What they consistently found is that modern Egyptians are about twice as much Sub-Saharan African as ancient Egyptians. The proportions for modern Egyptians ranged from ~10 to ~20 percent Sub-Saharan African against a Eurasian background, with a bias toward the higher values (depending on which populations you put into the phylogeny for non-Africans), and ~0 to ~10 percent for the ancient Egyptians, again with a bias toward the higher values. The pattern is consistent in these tests.

An issue here is that we’re going off three samples. That being said, the authors observe that despite differences in contamination/quality and time period they’re very concordant with each other. If I had to bet I think Old Kingdom samples would have somewhat less Sub-Saharan and eastern farmer ancestry. But the basic pattern persisted down to the Roman period, and was only shifted by admixture due to slavery.

And not to belabor the point, but a paper from a few years ago which had some Copt samples looks familiar in its broad outlines. You see that the Copts have very little Sub-Saharan African ancestry, though it does seem to be evident (the marker set is in the hundreds of thousands of SNPs). Additionally, they are quite distinct from the Qatari Arab sample.

Unfortunately the data for this paper just published is not on the European Nucleotide Archive. I really want to dig a little deeper into it.

What are the takeaways here? Egypt has been the sink for a lot of migration and gene flow over the past several thousand years, and probably earlier. Not surprising considering that it was relatively wealthy in the aggregate. The Natufian population that the Late Period Egyptians resemble the most did not have Sub-Saharan African ancestry according to earlier research. These Late Period Egyptians do have some. This is reasonable in light of the long interaction with Nubia which is historically attested. Similarly, there was clearly gene flow from Southwest Asia. This is again historically attested, especially in the Nile Delta (though foreign garrisons of mercenaries are recorded in Upper Egypt as well).

The Roman period probably did introduce some gene flow from Southeast Europe and Southwest Asia. But these populations are not that distinct from Egyptians.

Similarly, the Islamic period also brought in different peoples from Arabia and the Caucasus. But the most salient dynamic during the Islamic period was a massive trans-Saharan slave trade (though the Caucasus impact may have been comparable, and I think these results support the proposition that it was).

It seems entirely likely that the Copts are descended from a mix of Roman era Egyptians. Not only do they resemble the people in the Fayum portraits, but the circumstantial genetic data is that they have fewer “exotic” components which increased in frequency during the Islamic era. This would be exactly parallel to ethno-religious minorities in the Levant and Iraq.

One curious element to me is the suggestion gene flow before ~5,000 BCE between Sub-Saharan Africa and the lower Nile valley was low. If it hadn’t been low, it seems unlikely that the fraction of Sub-Saharan ancestry (or shift in that direction in relation to other Eurasians) in Copts would be so small.

So what explains the lack of earlier gene flow? I think the answer is going to be the fact that the human demographic landscape is characterized by lots of local population extinctions. As ancient DNA sampling coverage gets better and better meta-population dynamics are coming into focus, and we see gene flow, and die offs, in several areas. It is fashionable to say that human population variation is characterized by clines. But much of this clinal aspect is an outcome of the period after massive admixture over the last ~10,000 years.

And yet it may not be that the period before the Holocene was not clinal. Rather, it may be that large depopulations of areas of human occupation fragmented clinal ranges, and resulted in new range expansions from “core” zones.

About ~8,000 years ago there was a major desertification period in the Sahara desert. Many trans-Saharan populations may have gone extinct during this time due to rapid climate change. Eventually repopulation may have occurred from outside of the Sahara, so that post-Natufian Levantines and Sub-Saharan Africans from what today call the Sahel pushed up and down the Nile drainage basic respectively, meeting in the zone of Nubia on the boundary of history and prehistory.

Unlike many other areas of the world we have a long attested record of Egyptian history. As we get more mummy samples it seems likely that we’re get a crisper, clearer, picture. And the time transects will not be narrative blind; we already know the general arc of Egyptian history. If, for example, we see a new ancestral component around ~1500 B.C., in Egypt it’s not mysterious what this might be: the Hyksos.

This is just the prologue to a fascinating book that will be written over the next decade.

Related:Blog post analyzing one Copt’s results suggests that Sub-Saharan admixture is more like Dinka than Yoruba (in contrast, Muslim Egyptians have a mix of both, the latter probably coming during the Islamic slave trade, while the former is probably ancient admixture).

July 7, 2011

As many of you know when you have two adjacent demes, breeding populations, they often rapidly equilibrate in gene frequencies if they were originally distinct. There are plenty of good concrete examples of this. The Hui of China are Muslims who speak local Chinese dialects. The most probable root of this community goes back to the enormous population of Central Asia Muslims brought by the Mongol Yuan dynasty that ruled ruled China for over a century from the late 1200s to 1300s. Genetic studies of this group that I’ve seen indicate that a high bound estimate for West Eurasian ancestry is ~10%. The other ~90% is interchangeable with the Han Chinese. So let’s assume that the Hui are ~10% West Asian. If you assume that in the year 1400 the Hui were “pure,” you have 24 generations (25 years per generation). The original population of “Central Asian Muslims” were heterogeneous, including Iranians and Turks. But let’s take it granted that they were 50% East Eurasian and 50% West Eurasian in ancestry at the time of their arrival. What would the intermarriage rate per generation have to be so ...

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November 17, 2010

Dienekes Pontikos keeps chugging along, and has cranked out a new bar plot from the ADMIXTURE program with 15 putative ancestral components. He has “69 populations, and 1,189 individuals in total.” Most of these were assembled from public data, but some of them are particular to the Dodecad Ancestry Project. He contends:

In comparison to the K=10 analysis, the increased resolution allows us to:

- South Asians belonged primarily to the South Asian and West Asian components; this South Asian component spilt over to Iran and Central Asia. Now, a new Central-South Asian component, corresponding to the Ancestral North Indian of a recent study is inferred, and a corresponding South Indian component.

- HGDP Bedouins and Behar et al. (2010) Saudis take up their own component which I labeled Arabian. This appears to be a subset of the Southwest Asian component of the K=10 analysis

- There are several components in Siberian and Central Asian populations, alread discovered in my regional analysis. These are Central Siberian, Nganasan, Koryak, Chukchi, and Altaic which replace the K=10 Northeast Asian component

Not only has he generated a bar plot, but there is a PCA showing the relationship between the 15 ancestral groups, as well as a hierarchical tree. Since he references to the ANI and ASI of Reich et al., I thought I would note that the South Indian element from Dienekes’ K = 15 is still found in appreciable portions in the Turkic groups which earlier exhibited the South Asian component. And, on the PCA and phylogenetic tree it still clusters with West Eurasians more than East Eurasians, which is not the case with ASI (or the various Indian mtDNA lineages which coalesce back to a more recent common ancestor with East Eurasians).

The bar plot is below. Of interest are the most “pure” European groups, the Sardinians and Lithuanians. Also, compare Scandinavians and Finns.

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November 3, 2010

If you haven’t, you should keep an eye on Dienekes‘ Dodecad Ancestry Project (RSS). The pilot phase of data collection is over, and the first population level statistics are now coming out. Of particular interest to me is a new analysis of various northern European ethnicities just published.

The samples used in this analysis are:

- 25 HapMap-3 White Americans. These are the Mormons of predominantly Northwest European heritage

- 5 Dodecad Project Finns

- 25 HGDP-CEPH Russians from Vologda, in north-central European Russia

Below are two visualizations of the genetic structure. First, an MDS. And second, a bar plot of ancestral quanta derived from ADMIXTURE. I’ve added some clarifying labels.

Remember that the data you input into these analyses shape the nature of the outcomes to some extent. All these populations are very genetically close when scaled to average worldwide inter-population genetic variation. So what Dienekes is smoking out here are subtle differences between relatively close groups.

The first clear result supports previous research using uniparental markers: the ethnogenesis of the “Great Russians” involved both demographic expansion, and, cultural assimilation. The process on the southern and eastern frontiers is well documented, because it continued into the early modern period via a series of private wars of expansion. Turkic and Ugric groups were defeated by “Cossacks”, and often themselves integrated into the Cossack population as it expanded further into Siberia and the Steppe. Lenin’s paternal grandmother for example is often claimed to have been a Kalmyk, a branch of the Dzungar Mongol Confederacy which had settled in the lower Volga region. Whatever the truth, Lenin’s father clearly had an Asiatic cast to his features. The ancestral quanta estimates always seem to show that Russians, though not other Slavs further to the west, seem to average around ~5% or so “eastern” ancestry (by analogy, this is about the amount of African ancestry in the typical Levantine Arab).

But the expansion into the Finnic north is less well documented. To some extent the process of Russification began far earlier, as even Kievan Rus at the turn of the first millennium has been claimed to have had Finnic elements (the Rus were Swedes, but they probably picked up Finns in their warbands as they swept south, in addition to the numerous indigenous Finnic groups in northeast Europe). Additionally, unlikely the Muslim Turks these Finnic groups were often small-scale societies without international connections or affiliation with any “higher civilization” which could serve as an oppositional ideology to Orthodox Russian culture. The wide geographic expanse of the Russian ethnos means that one must be exceedingly sensitive to sample representativeness. Readers of Russian or Finnish origin are often aware of which localities in northern Russia were only recently Slavicized, and so express caution in comments as to utilization of those samples as representatives of Slavs more generally.

The second peculiarity are the “Germans” who affiliate with the Finns in the MDS, and contribute to the Finnish element among the Germans. Dienekes says: “without revealing any information, I’ll just say that this is contributed primarily by 3 Dodecad Project members who deviate towards Finns and whose ADMIXTURE analysis shows a higher than expected Northeast Asian component. Their outlier status is also visible in the MDS plot.” By “Northeast Asian” he presumably means one of the 10 ancestral components he’d found in earlier analyses. Without any more information I assume there’s a high probability that these are simply Germanized part-Sami. Much of northern Scandinavia was inhabited by Sami down to the early modern period. For example, the Sami were ethnically cleansed and assimilated across the north half of what is today Sweden as late as the 1600s and 1700s. Though I haven’t done the requisite reading, I wouldn’t be surprised if this was just a function of more advanced farming techniques as well as hardy New World crops such as potatoes which pushed the possible limits of Swedish settlement north.

Finally, there’s a clear Finnic component in the results. As Dienekes noted this Finnic component itself may be a composite of East and West Eurasian elements, just as the South Asian component in Eurasia may be a composite of “Ancient North Indians” and “Ancient South Indians.” One thing to remember about the Finnic component is there’s evidence for a fair amount of genetic variation within Finland. Representativeness is probably key here, just as it is for Russians. Ethnic Finnish individuals with ancestry along the southern and western coasts probably have more affinity with Germanic populations than Karelians.

For many decades there have been arguments as to the provenance of the Finns. Specifically, are they outsiders to Norden who arrived from the east, bringing with them their language? Or are they are indigenous vis-a-vis Germanic speakers? The past is complex, so a simple model is going to shave off a lot of the detail, but I suspect that the truth is closer to the second. It seems that the Finnic groups, or at least their languages, have an ultimate origin in Central Eurasia after the last Ice Age. But they are possibly a circumpolar population which expanded north and practiced hunter-gatherer lifestyles following the ice sheets. Over time agriculturalists expanded north and squeezed them on the margin, but I believe there were natural ecological limits to the practice of techniques derived from Middle Eastern crops. Though northern Finns adopted some agricultural techniques, there was enough of a slowdown of the spread agriculture by Indo-European speakers and their precursors that they managed to hold their own in the north. In much of European Russia, and later in pre-19th century Finland, we see plenty of evidence of language-switching from Finnic to Indo-European (in Finland nationalism resulted in a back-switch over the past 150 years). If the Malthusian pre-modern age had persisted for another two or three centuries I would not be surprised if Finnic languages were totally absorbed by Russian and Scandinavian Indo-European dialects. As it is, 19th century language based nationalism stopped the process of elite culture assimilation, and in some cases reversed it (many elite Finland Swedes abandoned Swedish language and identity in the 19th and early 20th centuries).

Addendum: The picture I present above is simple, and I don’t believe it captures a lot of what happened. For example, from my reading there was a pause of about 1,000 years in the expansion of agriculture once it reached the Kattegat between Denmark and Sweden. I suspect that these long pauses were a function of ecology and geography, as they’re often just too long to be determined by social-political inertia. Additionally, it seems unlikely to me that the first agriculturalists in Europe were Indo-European speakers. Rather, that is possibly a subsequent linguistic overlay, especially in the western regions of Europe.

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September 19, 2010

If you live in the States one of the things you hear a lot about Europe in regards to its relationship to its ethno-religious minorities are the problems with Muslims. This is probably an Americo-centric perspective shaped by 9/11, when many of the hijackers had turned out to have spent time in Germany. Additionally, terrorist actions in both London and Madrid highlight the persistence of these problems over the years. These sorts of shocking events put a sharp focus on the geopolitical cross-hairs which Europe finds itself in in the second age of mass migration. Though this time it is a destination, and not a source.

But having been to Europe recently it was notable that in several regions the day-to-day tension when it came to ethnicity often focused on Gypsies (I use the older term because the ethnonym “Roma” which has become politically correct in the USA includes only a subset of Europe’s Gypsy population, even if the greater number). Many regions of Europe now have two distinct populations of Gypsies, a long resident local group, as well as Roma from the eastern nations of the EU. Though the relationships between these traditionally nomadic peoples and indigenous populations has never been without tension, it is clear that something close to a modus vivendihas been achieved in many European nations between the majority and their small native Gypsy populations. The influx of the Balkan Roma add a new variable.

But the political fuss for me simply rekindled a curiosity as to the genetic origins of the Gypsies. Culturally their South Asian provenance couldn’t be clearer; they speak an Indo-Aryan language. Their term for themselves in many parts of Europe comes from the Indo-Aryan word for “black,” as they are are darker than the natives of the lands in which they have settled , and in fact often look visibly South Asian. This seemed especially true of Balkan Roma. On the other hand the Kale of Finland looked to be brunette Europeans.

The problem with the genetics of the Gypsy people of Europe is that until recently they’ve focused on uniparental lineages. Though this has confirmed their South Asian origins, looking at maternal or paternal direct descent alone leaves something to be desired in terms of assessing ancestry, and, these two markers (mtDNA and Y) are subject to more drift as they are haploid (half as many copies). But a new paper in The American Journal of Physical Anthropology has some results using 16 autosomal STRs (a group of highly variant markers). A Genetic Historical Sketch of European Gypsies: The Perspective From Autosomal Markers:

In this study, 123 unrelated Portuguese Gypsies were analyzed for 15 highly polymorphic autosomal short tandem repeats (STRs). Average gene diversity across the 15 markers was 76.7%, which is lower than that observed in the non-Gypsy Portuguese population. Subsets of STRs were used to perform comparisons with other Gypsy and corresponding host populations. Interestingly, diversity reduction in Gypsy groups compared to their non-Gypsy surrounding populations apparently varied according to an East-West gradient, which parallels their dispersion in Europe as well as a decrease in complexity of their internal structure. Analysis of genetic distances revealed that the average level of genetic differentiation between Gypsy groups was much larger than that observed between the corresponding non-Gypsy populations. The high rate of heterogeneity among Gypsies can be explained by strong genetic drift and limited intergroup gene flow. However, when genetic relationships were addressed through principal component analysis, all Gypsy populations clustered together and was clearly distinguished from other populations, a pattern that suggests their common origin. Concerning the putative ancestral genetic component, admixture analysis did not reveal strong Indian ancestry in the current Gypsy gene pools, in contrast to the high admixture estimates for either Europeans or Western Asians.

This isn’t a 500,000 SNP-chip analysis, so everything needs to be taken with a grain of salt. But, 16 markers is a lot more than the two you usually have to deal with when assessing the genetics of the Gypsy populations of Europe, so it’s certainly an improvement when making inferences. One figure and table are really worth looking at in this paper.

The first plot shows the variance partitioned into two dimensions as a function of the 13 STRs. The table shows bootstrapped admixture estimates and standard deviations. They had a 3-population model with West Asians, but it didn’t look to me like they were getting sensible results with that, so I excised that portion (with only 600 pixels the table would have been very hard to read with the nonsensical estimates in). I think the last model where they aggregate West Asians with Europeans makes the most sense. I assume the major issue here is that with 16 STRs which aren’t necessarily filtered for ancestral informativeness within these populations you’re going to get weird results on the margins.

These results confirm the finding from previous Y and mtDNA results that Europe’s Gypsy populations are genetically fragmented, and seem to have gone through bottlenecks. In this paper they also seem to have found a pattern of decreased genetic variance from east to west for the Gypsy groups, which makes sense in light of a historical model of serial bottlenecks as they traversed Europe. Any reasonable model of the genetic heritage of the Gyspy people of the world posits that they’re a compound to various extents of populations distributed along a continuum between South Asia and Western Europe, and yet here you see a 2-dimensional plot that they don’t look like a linear combination of South Asians and Europeans. Why? Because of their unique genetic history has resulted in their “random walk” into patterns of allelic variance distinct from the ancestral groups.

But a second genetic dynamic with these populations seems to be admixture. With 16 STRs, and obvious sensitivity depending on the populations you survey, one should be careful about overweighting the findings from this paper. And yet plausibly it does show a pattern of decreased South Asian admixture the further you go from the Balkans. Not only does this stand to reason a priori, but empirically it’s generally agreed that the Gypsy groups of the north and west of Europe look less South Asian in appearance than those of the Balkans.

A final consideration here is that the Indian populations which they used as a reference for South Asians are not representative of the ancestral Indian groups from which Gypsies derived. The Indo-Aryan language of the Gypsies seems to share the most features with the language of northwest India, Punjabi and Hindi. But the samples which had the appropriate STRs for comparison were Central and South Indian. Overall I don’t think that’s that much of a consideration, but something to remember.

A bigger take home point is the disjunction between cultural and biological modes of inheritance and persistence. The language of the Gypsies retains in its broad outlines the character of an Indo-Aryan tongue. That is why the South Asian origins of Gypsies was able to be ascertained by Indian sailors in Britain who overheard, and broadly understood, what Gypsies were saying. Romanipen, the spirit of Gypsy culture which transcends difference of religion and nationality, seems to be clearly traceable to some South Asian antecedents (e.g., the emphasis on avoidance of contamination of food by outsiders).

And yet despite the cultural distinctiveness the various Gypsy populations have become genetically less South Asian. That makes sense, it seems likely that they left India ~1000 years ago, or 40 generations. They’ve been in the Balkans for about 600 years, or 24 generations. Let’s assume unrealistically that the Roma were 100% South Asian when they arrive in the Byzantine lands (there are related groups in the Middle East, so it seems certain they picked up Middle Eastern ancestry along the way, but no matter). 99% endogamy per generation would imply that they’d be 79% South Asian today. 95% endogamy would result in them being 29% South Asian. 90% endogamy would mean that they’d be 8% South Asian. Reality is more complex. It is likely that in the early periods when social norms had not hardened and Roma were less numerous the endogamy rates were probably far lower, especially as the Gypsy bands mixed with other destitute groups in the Balkans. The evidence of lots of structure across the Gypsy groups points to endogamy drilling down to a lower level of organization than just the ethnic group, which would be consistent with tendencies within South Asian culture more broadly.

More generally it seems that the Roma and their relatives can’t just be understood as a simple linear combination of Europeans, Middle Easterners, and South Asians, genetically or culturally. Their unique history has reshaped them, and their persistence and demographic expansion in the face of ostracism and persecution are clear evidence as to the functional success of their social-cultural traditions.

The Comoros Islands are situated off the coast of East Africa, at the northern entrance of the channel of Mozambique. Contemporary Comoros society displays linguistic, cultural and religious features that are indicators of interactions between African, Middle Eastern and Southeast Asian (SEA) populations. Influences came from the north, brought by the Arab and Persian traders whose maritime routes extended to Madagascar by 700–900 AD. Influences also came from the Far East, with the long-distance colonisation by Austronesian seafarers that reached Madagascar 1500 years ago. Indeed, strong genetic evidence for a SEA, but not a Middle Eastern, contribution has been found on Madagascar, but no genetic trace of either migration has been shown to exist in mainland Africa. Studying genetic diversity on the Comoros Islands could therefore provide new insights into human movement in the Indian Ocean. Here, we describe Y chromosomal and mitochondrial genetic variation in 577 Comorian islanders. We have defined 28 Y chromosomal and 9 mitochondrial lineages. We show the Comoros population to be a genetic mosaic, the result of tripartite gene flow from Africa, the Middle East and Southeast Asia. A distinctive profile of African haplogroups, shared with Madagascar, may be characteristic of coastal sub-Saharan East Africa. Finally, the absence of any maternal contribution from Western Eurasia strongly implicates male-dominated trade and religion as the drivers of gene flow from the North. The Comoros provides a first view of the genetic makeup of coastal East Africa.

In the paper they note that ~6% of the Y chromosomal lineages were Southeast Asian, while ~15% of mtDNA lineages were. That indicates that the Southeast Asian presence on the Indian ocean was a case of folk migration, men, women and children on the move. The data from Madagascar indicate something similar, both male and female lineages show Southeast Asian imprint among the highland Malagasy (I don’t make much of the proportional difference because this is just one sample). In contrast, they show in this paper that there’s a substantial West Eurasian (probably Arab, Indian and Persian) Y chromosomal gene flow into the population of Comoros, but no West Eurasian mtDNA. So in this case you have a clear contrast with that of the Southeast Asian seafarers, the Muslim merchants who settled on the Comoros did not bring their children or womenfolk. It was not a folk migration, but a mercantile network. Because of the nature of the sources, and the cultural influence of the West Asians, we know of their presence from the historical record. In contrast, the arguably more substantial folk migration of Southeast Asian seafarers from Borneo is hidden in the text. They may have been of no concern or beneath mention from the perspective of the Muslim merchant princes, but the fact that they were no longer on the high seas by the time the Portuguese arrive may also indicate that they were driven off by the same Muslim merchant princes in the years after 1000. If the latter is the case the silence may be due to the inclination to forget an unpleasant rivalry.

All this goes to show that history’s reliance on text can mislead and obscure real dynamics. Even social and economic history which attempts to tunnel-down to the level of the populace is still heavily reliant on written records. In the case of seafarers it seems likely that even archaeologists would be unable to detect their movements because of the liminal nature of their settlements. The linguistic and cultural influences in Madagascar and in East Africa indicate a sojourn by Austronesians in that coast, but there is no physical or textual record. There is the “dark history” which we ignore because of current ideological preferences, and then there is the dark history which has fallen outside of our methodological window.

June 6, 2010

Over at Discover Blogs I have a very long post up on Jews & Genetics. In particular the recent paper in AJHG. One observation I have to make about Jewish genetics: when it comes to PCA plots which illustrate the relationship of Jews, in particular Ashkenazi Jews, to other populations I’ve noticed that two different individuals can look at the same plot and reach diametrically opposite conclusions. For example, “this plot shows that Jews are European” vs. “this plot shows that Jews are not European,” where “this plot” refers to the same plot. An interesting illustration of the importance of interpretative frames when it comes to distilling the valid inferences from results.

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April 30, 2010

I am currently reading Peter Heather’s Empires and Barbarians: The Fall of Rome and the Birth of Europe. This is a substantially more hefty volume in terms of density than The Fall of the Roman Empire: A New History of Rome and the Barbarians . It is also somewhat of a page turner. One aspect of Heather’s argument so far is his attempt to navigate a path between the historically tinged fantasy of what its critics label the “Grand Narrative” of mass migration of barbarian tribes such as the Goths, Vandals and Saxons during the 4th to 6th centuries, dominant before World War II, and its post-World World II counterpoint. As a reaction against this idea archaeologists have taken to a model of pots-not-people, whereby cultural forms flow between populations, and identities are fluid and often created de novo. This model would suggest that only a tiny core cadre of “German” “barbarians” (and yes, often in this area of scholarship the most banal terms are problematized and placed in quotations!) entered the Roman Empire, and the development of a Frankish ruling class in the former Gaul, for example, was a process whereby Romans assimilated to the Germanic identity (with the shift from togas to trousers being the most widespread obvious illustration of Germanization of norms). I believe that liberally applied this model is fantasy as well. Being a weblog where genetics is important, my skepticism of both extreme scenarios is rooted in new scientific data.

There are cases, such as the Etruscans, where the migration is clear from the genetics, both human and their domesticates. The peopling of Europe after the last Ice Age is now very much an open question. The likelihood that the present population of India is the product of an ancient hybridization event between an European-like population and an indigenous group with more affinity with eastern, than western, Eurasian groups, is now a rather peculiar prehistoric conundrum. It also seems likely that the spread of rice farming in Japan was concomitant with the expansion of a Korea-derived group, the Yayoi, at the expense of the ancient Jomon people. And yet there are plenty of inverse cases. The spread of Latinate languages and Romanitas did not seem to perturb the basic patterns of genetic relationship among the peoples of Europe. The emergence of the Magyar nation on the plains of Roman Pannonia seems to have involved mostly the Magyarization of the local population. In contrast, the Bulgars were totally absorbed by their Slavic subjects culturally, leaving only their name. The spread of the Arabic language and culture was predominantly one of memes, not genes (clearly evident in the current dynamic of Arabization in parts of the Maghreb).

And yet you will note that there is a slight difference between the few examples I’ve cited: population replacement seems to have occurred in the more antique cases, rather than the more recent ones. This would naturally bias the perspectives of historians, who have much more data on more recent events (no offense, but archaeologists seem to be able to say whatever they want!). The Etruscan language itself is known only from fragments, while the happenings in prehistoric Europe and India can only be inferred very indirectly. I now offer a modest hypothesis for the distinction, why in some cases is it just the “pots” which move (Arabs), and in other cases it is the people who move (the Japanese). In cases of population replacement there is often a shift in mode of production. In cases where there is the diffusion of culture it is often a system or set of ideas which rent-seeking elites can exploit to maintain their position, or perpetuate it, flow across space. Islam was not only a potent ideology which bound the tribes of Arabia together so that they could engage in collective action, local elites across the new Muslim-dominated world found it a congenial international system whereby they could integrate themselves into a civilization of elite peers, as well as justify their god-given position at the apex of the status hierarchy (granted, many had this in the form of Christianity or Zoroastrianism, but once the old top dogs were overthrown the benefit of these systems was considerably less). The spread of Yayoi culture in Japan involved a shift from more extensive, toward more intensive, forms of agriculture. Their population base was greater, and the domains of the Jomon were left “underexploited” from the perspective of the more productive mode of agriculture which the Yayoi were engaged in. It need not be an issue of mass slaughter or extermination, a high endogenous rate of natural increase as well as disease, combined with assimilation and co-option of local elites, could result in the swallowing up of a population engaged in a less intensive mode of production. This sort of hybrid aspect of cultural and genetic expansion, whereby the local substrate is assimilated and synthesized with the expanding ethnic group, seems to be a good fit to the pattern that we see among the Han of China.

But shifts from modes of production exhibit some level of discontinuity, insofar as there are diminishing returns once all the land appropriate for that mode of production has been taken over. Farmers who are expanding into land held by hunter-gatherers or those practicing less intensive forms of agriculture can have enormous rates of natural increase because they’re not bound by Malthusian constraints. This is evident in the United States, until the late 20th century the majority of the ancestry of the white population of the republic descended from those who were counted in the 1790 census. The reason had to do with the extremely high birthrates among white Americans. When regions such as New England were “filled up,” they pushed out to the “frontier,” to northern Ohio, then to the Upper Midwest, and finally the Pacific Northwest. And in the process there was a radical change in the genetic variation of North America, as the indigenous populations died from disease, were numerically overwhelmed, or genetically absorbed. This is an extreme case scenario, but I think it illustrates what occurs when modes of production collide, so to speak. The pattern in Latin America was somewhat different, though an amalgamated Mestizo population did emerge over time, there was not the wholesale demographic replacement in many regions. And I believe that the reason is that the Iberians did not bring a superior mode of production, rather, the large local population base engaged in agriculture presented an opportunity for rent-seekers to place themselves atop the status hierarchy. Sometimes this involved intermarriage with local elites, as was the case in Peru where the nobility of the Inca intermarried with the Spanish conquistadors for the first few generations (the whiteness of the Peruvian elite despite the fact that the old families have Inca ancestry is simply due to dilution as successive generations of lower Spanish nobility set off to the New World and married into Creole families).

By the Roman period I believe that much of the core Old World was “filled up” in terms of intensive agricultural production. So most, though not all, of the changes in ethnicity or identity are biased toward elite emulation and novel identity formation. The Turks did not bring an innovative new economic system whereby they replaced the Greek and Armenian peasantry in Anatolia, rather, on the contrary peculiarities in the Turkish Ottoman system of rule produced a situation where the old families were usually replaced in positions of power by converts from the Christian groups who assimilated to a Turkish identity. When the economic arrangements reach stasis and the population is at Malthusian equilibrium change is a matter of shifting identities and affinities of the rent-seekers. When radically new economic systems emerge, opportunities for disparate population growth present themselves. Ergo, England went from being demographically dwarfed by France in the 17th century, to surpassing it in population in the 19th. England was of course the first nation to break into a new mode of production since the agricultural revolution.

Credit: Thanks to Michael Vassar for triggering this line of reasoning after a conversation we had about the Neolithic revolution.

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April 20, 2010

Jared Diamond famously argued in Guns, Germs and Steel that only a small set of organisms have the characteristics which make them viable domesticates. Diamond’s thesis is that the distribution of these organisms congenial to a mutualistic relationship with man shaped the arc of our species’ history and the variation in wealth that we see (though his a human-centric tale, we may enslave them, eat and use them as beasts of burden, but these are also species which have spread across the world with our expansion). This thesis has been challenged, but the bigger point of putting a focus on how humans relate to their domesticated animals, and the complex co-evolutionary path between the two, is something that we need to consider. In a plain biological and physical sense animals have utility; we eat them, and for thousands of years they were critical to our transportation networks. Some have argued that the rise of Islam, Arab monotheism, was contingent on the domestication of the camel (which opened up interior trade networks previously unaccessible). In The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World the argument is made that the distribution of the Indo-European languages has to do with the facility of Central Eurasian plainsmen with their steeds. And of course there is the domestic dog, arguably the one creature which is able to read our emotions as if they were a con-specific.

I suspect that the evolution and ethology of domesticated animals will offer a window into our own evolution and ethology. Konrad Lorenz famously believed that humans were going through their own process of domestication all the while that they were selecting organisms suited to their own needs. More pliable, less intelligent, faster growing and maturing, and so forth. Know thy companions, and know thyself, so to speak.

What about an animal as intelligent as a dog, but famously tasty? (the combination of the two characters causing some ethical tension in the minds of many) I speak here of the pig. A few years ago research came out which showed that pig-culture was introduced to Europe from the Middle East. That is, Middle Eastern pigs came with Middle Eastern people in all likelihood. But modern European pigs do not derive from these lineages, rather, by comparing modern genetic variation with ancient DNA the authors showed that the Neolithic pigs had been replaced by local breeds. Just as pigs can go feral and fend for themselves rather easily, it seems that their basic morph can be derived from wild boar populations easily as well (by contrast, it will perhaps take some effort to derive a pekingese from wolf populations, offering a reason for why small dogs seem to have emerged once). A new paper explores the evolutionary history and phylogeography of the pigs of the swine-loving societies par excellence, those of East Asia. Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA:

The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (Sus scrofa) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as “cryptic domestication,” given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.

They used conventional phylogeographic techniques to catalog the variation in modern populations, as well as supplementing their data set with ancient samples. Here the genetic variance they’re looking at is the mtDNA, the maternal lineage. Easy to get at, and easy to analyze (lots of it, and non-recombinant). In general they seem to have found that there is a common genetic heritage of East Asian domestic pigs, who are embedded geographically among varieties of wild pig who exhibit localized genetic variants. Additionally, there are other varieties of domestic pig in Southeast and South Asia who seem to have arisen from their own boar populations (though there is a Pacific pig variant which seems to have been from mainland Southeast Asia, but that original source population has now been replaced by East Asian pigs). Finallythey find a strong continuity between ancient domestic East Asian pigs and the modern populations. This is a contrast with the findings in European which exhibited disjunction between past and present. Perhaps this has to do with the fact that East Asian pigs are more genuinely indigenous, derived from local wild lineages with regional adaptations, while the Middle Eastern pigs brought to Europe were short-term kludges easily superseded by domesticates derived from European boar populations.

This figure shows the nature of haplotype sharing between wild and ancient & contemporary domestic pigs. The larger the pie, the more frequent the haplotype. The slices of the pie by color show wild (black), ancient (red) and modern domestic (white) shares of that haplotype. The line across the networks show the putative separation between the genetic variants relatively private to the wild populations, and those which lean toward a mix of wild & domesticates. The wild populations seem more diverse. 45 haplotypes out of 167 samples are found only in wild specimens, 92 haplotypes out of 339 samples are found only in domestic specimens, and 21 haplotypes are found in both 87 wild and 582 domestic pigs. One assumes that the domesticates are derived from a small subset of wild pigs, and that population underwent demographic expansion within the last 10,000 years. That’s not too different from our species, we’re descended from a small subset of H. sapiens, and we’ve undergone major demographic expansion. Our “wild” cousins among the great apes tend to have a lot more genetic variation even within their small populations because their demographic history has presumably been a bit more staid. As man was, so shall he turn his domesticates. And yet a major difference between the domestic pig and man seems to be that some variant of multiregionalism, the evolution of modern pigs from local lineages, and their subsequent hybridization to produce a genetically unified species, has been operative. One major caution with these studies is that they’re looking at mtDNA. The dog genomics work has been modified and overturned when they shifted from the mtDNA that most phylogeographers focus on to the total genome. One does not know the evolutionary history of an organism by one locus alone.

The pig is a peculiar beast, retaining its feral nature as evident by the periodic reemergence of morphs from released domestic populations which have no difficulty in going “wild.” There are 4 million feral hogs in the United States, and they can get quite large indeed. What would the pekingese do in a world without man? Probably be some other creature’s meal. But generalists like the pigs would no doubt flourish. The story of the pig is a story of piggybacking, so to speak, on the success of the upright ape and spreading across the world on the backs of the other white meat.

Let me finish from the author’s conclusion:

The evidence presented here suggests the following evolutionary history of pigs in East Asia. Having originally evolved in ISEA [Island Southeast Asia], wild Sus scrofa migrated (without human assistance) across the Kra Isthmus on the MalayPeninsula into Mainland Asia. From here, they spread across the landscape and, after traveling over land bridges, onto the islands of Japan, the Ryukyu chain, Taiwan, and Lanyu where they evolved unique mitochondrial signatures. After millennia of hunting and gathering, a major biocultural transition occurred early in the Holocene during which human populations in East Asia domesticated a variety of plants and animals, including pigs. This process took place at least once in the Yellow River drainage basin wheremilletmay have been first domesticated as early as 10,000 B.P…and may have also taken place independently in the downstream Yangtze River region where rice may have been domesticated…Two things are clear from the ancient DNA evidence presented here. First, unlike Europe, modern Chinese domestic pigs are the direct descendants of the first domestic pigs in this region. Second, despite the occurrence of a genetically distinct population of wild boar throughout modern China, this population has neither been incorporated into domestic stocks nor exterminated.

In this book I have offered a synthesis of genetic and other evidence. Everything points to a single southern exodus from Eritrea to the Yemen, and to all the non-African male and female gene lines having arisen from their respective single out-of-Africa founder lines in South Asian (or at least near the southern exit). I regard the genetic logic for this synthesis as a solid foundation, and I have based the rest of my reconstruction of the human diaspora upon it. Obviously, the ‘choice’ of starting point (mine or theirs) determined all the subsequent routes our ancestors and cousins took. Tracing the onward trails is only possible as a result of marked specificity in regional distribution of the genetic branches The geographic clarity of both male and female gene trees is a big departure from the fuzzy inter-regional picture shown by older genetic studies. The degree of segregation of lines into different countries and continents is in itself good evidence that once they got to their chosen new homes, the pioneers generally stayed put, at least until the Last Glacial maximum forced some of them to move. This conservative aspect of our genetic prehistory also provides a partial explanation for the fact that when we look at a person, we can usually tell, to the continent, where their immediate ancestors came from, and underlies differences that some of us still call ‘race.’

Oppenheimer wrote the above in the early aughts, as his book was published in 2003. Much of this is generally in line with the ‘orthodoxy’ of the day. I believe that Oppenheimer’s assertion that there was one southern migration out of Africa by anatomically modern humans has gained some advantage over the alternative model of two routes, northern and southern, over the past ten years (Spencer Wells’ The Journey of Man sketches out the two wave model). Other assertions and assumptions have not stood the test of time. In particular, I would contend that generally the ‘conservative aspect of our genetic prehistory’ can no longer be taken for granted. Specifically, it seems likely now that much occurred after the Ice Age and during the Neolithic.

The false inferences of the early aughts were due to two primary problems. First, they relied heavily on the powerful new techniques of extraction and analysis of uniparental ineages; the male and female direct line of descent. Concretely, mtDNA and the nonrecombintant portion of the Y chromosome. The lack of recombination allows for relatively easy reconstruction of phylogenies assuming a coalescent model. Second, the inferences attempt to make connections between the patterns of variation in modern populations, and what one may infer about the past from those patterns. Obviously constructing a phylogeny, or plotting haplogroup frequencies as a function of geography, is rather straightforward science. But using these results to generate inferences of the past is often more of an art than a science, and implicit assumptions lurk behind the causal chains. Consider for example the utilization of modern Anatolian (i.e., Turkish) genetic variation as a reference for the expansion into Europe of Neolithic farmers from the Near East. This of course presumes that modern Anatolians are a good proxy for ancient Anatolians. There are various suggestive reasons for why this is a plausible assumption, but assemble enough plausible assumptions, and rely on their joint likelihood, and you construct a very rickety machinery of possibility.

In early 2007 I began to have serious doubts about the orthodoxy of genetic conservatism. The primary trigger was the story of the Etruscans. Here is the crux of the issue: there are two models for the origins of the Etruscans, first, that they were the pre-Indo-European autochthons of Italy, or, that they were the migrants from the eastern Mediterranean, in particular Anatolia. The second may seem an outlandish hypothesis, but there were several tendrils of evidence to support it. But perhaps the ’support’ which weighed most against it is that the fact that the Anatolian model has an ancient source, the Greek historian Herodotus. I should perhaps put historian in quotes as well, because Herodotus is often viewed more as a repeater of myths, and derided by some as the ‘father of lies’ (in this he stands in sharp contrast to contemporary perceptions of the ‘modern’ Thucydides, though revisionists have begun to challenge this narrative). In contrast, the model that Etruscans are indigenous to Italy, and that their ‘exotic’ foreign traits were simply acquired through trade and cultural diffusion, dovetailed well with the post-World War II ‘pots not peoples’ paradigm. That cultural change was ubiquitous, while at the same time populations were immobile. It was boring, prosaic, and conservative, and so an ideal null hypothesis.

But here it turns out that Herodotus was right, and archaeologists were wrong. Genetic analysis of modern Tuscans from isolated villages shows that some are surprisingly closely related to extant eastern Mediterranean lineages. Genetic analysis of Tuscan cattle showed that they were surprisingly closely related to extant eastern Mediterranean lineages of cattle. Finally, extraction of ancient Etruscan DNA showed that they were closely related to extant eastern Mediterranean lineages. The overlap was often with Anatolia, and combined with fragmentary linguistic and archaeological data, the evidence clearly points to an exogenous origin for the Etruscans. The boring null hypothesis was wrong. After these genetic stories gained prominence I went and reread recent archaeological texts on the Etruscans, and there were many models which showed exactly how Etruscan cultural uniqueness derived back to prehistoric Italy. It seems in hindsight that the prior assumption served as an interpretative filter, and people saw patterns that they were primed to see based on what they ‘knew’ to be the history of prehistoric and early Iron Age Tuscany.

Of course to refute the primacy of Oppenheimer’s conservative model of genetics one has to offer more examples than that of the Etruscans, and in particular, examples which are of greater scope and weight. I believe those examples exist. In the early aughts based on the mtDNA evidence the likelihood was that South Asian genetic variation is by and large a product of changes wrought upon the basic elements extant in the region around the end of the last Ice Age. The Y chromosomal data was more confused, though it did imply a closer relationship to groups in western Eurasia. But based on the mtDNA Oppenheimer posited a model whereby India was the mother of all non-Africans, that is, all non-African lineages derived from roots within the Indian subcontinent before the Last Glacial Maximum. This is at sharp variance with colonialist narratives of an Aryan invasion of the subcontinent, and the subjugation of the natives by quasi-European overlords, who are the ancestors of the moder upper castes. The charged ideological import of this model is transparently obvious.

Unfortunately the reality is likely more complex. I suspect that some form of Oppenheimer’s model is correct, insofar as South Asia was likely an important way station for modern humans as they left Africa, and pushed into other regions of Eurasia, on to Australasia and the New World. This interpretation does gain support from mtDNA, the direct maternal lineage. But a new analysis of South Asian genetic variation using a substantial proportion of the autosomal genome implies in fact that South Asians are possibly descendants of an ancient hybridization event between a native population with deep roots in the subcontinent, and a quasi-European population which was exogenous to the subcontinent.* Genetically the quasi-European population is quite close to northern Europeans, similar to the genetic distance between modern Finns and Italians, not trivial, but far closer than that between modern South Asians and Europeans. Was this the ancient Aryan invasion? I remain skeptical of this particular detail for various reasons, as I suspect that the history of the Indian subcontinent is in fact even more complex than has been assumed before (I think it is more likely that the quasi-Europeans came before the Indo-Aryans, who arrived late, and had a stronger cultural than genetic influence).

Finally, there is another region of the world where it seems likely that the old orthodoxies of genetic conservatism will be overthrown. That region is Europe. The scientific orthodoxy of deep time continuity is strong enough that it has percolated into the public consciousness, the leader of the British National Party even referred to the deep roots of white British in demarcating who he believed ‘indigenous people’ of the Isles were. But newer data is more supportive of the hypothesis that in fact Neolithic farmers who arrived from elsewhere are the likely ancestors of most Europeans, not the hunter-gatherers who remained after the Ice Age. Extraction of ancient DNA has yielded a set of results which simply are not explicable assuming the older models of genetic continuity, which were based on inferences made from modern population variation. If I had to hazard a guess, I would have some, though not high, confidence in the following story. First, the indigenous hunter-gatherers are assimilated or marginalized by waves of Neolithic farmers pushing out from the eastern Mediterranean. The demographic expansion does not necessarily sweep outward along a southeast-northwest axis, rather, it follows the Mediterranean and Atlantic fringes, as well as along river systems in the interior. Its impact is weakest in the northeast of Europe, where Middle Eastern crops are least suitable, and the natives have the most time to absorb the cultural toolkit of the newcomers so as to resist their advance. Second, and far later, there was another wave pushing out from the region of the Ukraine to the Volga, likely the ancestors of the Indo-Europeans. Tentatively I would contend that these were the carriers of the Kurgan culture, and also brought the allele for lactase persistence. Again, for ecological reasons the populations of the northeast Baltic and into the forests of northern Russia were most insulated from this push (and non-Indo-European languages persisted in Iberia down to Roman times, and specifically in the Basque-country down to modern times, though I suspect this is a function of distance). So modern European populations may be assumed to be tri-hybrid, first a synthesis of Middle Eastern farmers overlain upon the Paleolithic substrate, and second a synthesis of Indo-Europeans from the east overlain upon pre-Indo-European substrate. Unlike the case of India I suspect teasing out these patterns in modern populations is more difficult because the genetic distance between the three ancestral populations is far smaller than between the indigenous peoples of India before the quasi-Europeans arrived.

This leaves much of the world untouched by my speculations, but I believe showing that the genetically conservative null hypothesis is now in serious doubt in South Asia and Europe is sufficient to knock it from being a necessarily default assumption through which we must filter our interpretations. I do not believe that the reordering of human variation and the welter of population movement after the Ice Age was equivalent in effect to the Out of Africa migration, but I do believe that it was important enough to make the world of 2000 BCE very different from that of 15000 BCE in regards to genetic variation. In some cases, such as Central Asia from the Caspian to the Taklamakan the world of 2000 CE is fundamentally different from the world of 0 CE.

I will then end with a prediction, one in which I do not have much confidence, but which may no longer be wrong on the face of it with these new data in mind. Here is a passage from page 7 of Jared Diamond’s Guns, Germs, and Steel:

Initially, archaeologists considered the possibility that the colonization of Australia/New Guinea was achieved accidentally by just a few people swept to sea while fishing on a raft near an Indonesian island. In an extreme scenario the first settlers are pictured as having consisted of a single pregnant young woman carrying a male fetus…..

Let me stipulate that Diamond seems skeptical of the extreme model, but it illustrates the consensus that Australian Aboriginal populations are descended from the first settlers. That is, the modern populations of indigenous Australians are the direct descendants of those who swept Out of Africa along the fringe of the Indian ocean, through Southeast Asia, and arrived in Australia (more specifically, Sahul), on the order of 40 to 60 thousand years ago. From what genetic data I have seen this may be true. But I do not know of any extractions of ancient DNA, and it seems to me that the analysis of the phylogenetics of Australian Aboriginals is relatively sketchy. Therefore, I will suggest that within the last 10,000 years there has been a major new migration of people into Australia, and the modern range of genetic variation of Australian Aboriginals is significantly different from that of the populations of the Ice Age. I suggest this primarily because the dingo arrived within the last 10,000 years, more likely as recently as 4,000 years ago. With the expansion of the utility of ancient DNA extraction and analysis this question may be answered in the near future. I would still bet I’m wrong with the hypothesis I just offered, but I’m far less sure than I would have been 2 years ago.

* I say ‘quasi-European’ because the population may have origins outside of the boundaries of modern Europe at the Urals. Perhaps in western Siberia. Additionally, the idea of ‘Europe’ is relatively new, and exhibits little ancient cultural coherency.

Demographically we know that historically much of eastern Anatolia was dominated by Armenians. Many of the prominent Byzantine dynasties were of Hellenized Armenian lineages. I would predict that one will likely find that most of the Turks of eastern Anatolia would cluster with Armenians, just as those Turks from the west and coastal Anatolia might cluster more with Greeks, because it seems likely that the ethnogenesis of most Turks in Anatolia was a process whereby Greeks and Armenians assimilated to the identity of a small minority of eastern Turkish invaders.

Demographically we know that historically much of eastern Anatolia was dominated by Armenians. Many of the prominent Byzantine dynasties were of Hellenized Armenian lineages. I would predict that one will likely find that most of the Turks of eastern Anatolia would cluster with Armenians, just as those Turks from the west and coastal Anatolia might cluster more with Greeks, because it seems likely that the ethnogenesis of most Turks in Anatolia was a process whereby Greeks and Armenians assimilated to the identity of a small minority of eastern Turkish invaders.

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December 7, 2009

Historians often assume that the Romans changed Britain politically but not demographically. The indigenous elites adopted Roman culture while the mass of the population remained Celtic. When the Anglo-Saxons arrived in the fifth century, much of this population fled to Wales and Cornwall, where they would retain their language and traditions. Meanwhile, those who remained behind were obliterated through a process of ethnic cleansing and coerced assimilation.

This historical account may be false….

…

Once Rome had pulled its troops out of Britain in the early 5th century, there was no longer an inflow of people to offset the demographic deficit. The local population fell into decline, and the decline accelerated in the 6th century when plagues killed three out of every ten people. The Romano-British needed no help from the Anglo-Saxons to die out. They did it largely on their own.

Peter’s summation of the historical consensus is correct. This view is exposited in Norman Davies’ The Isles. The historians have had a bias for several generations of assuming that population movements have been marginal in shaping cultural change. In some cases this is correct; I’ve looked and it is very difficult to detect a discontinuity among the Hungarians in relation to their neighbors despite this nation’s putative origins among an Inner Asian group (and later settlement of Turks who fled the Mongols within the Magyar kingdom). The emergence of Hungarian is therefore most plausibly modeled as a process of elite emulation, where Romance, German and Slavic speaking peasants adopted the speech and identity of their Magyar overlords. The Hungarian case is easy to test because the geographical distance of the Magyar homeland in the Volga-Ural region is great enough that they would have been a genetically distinct population who would introduce alleles which couldn’t be explained except as exogenous inputs (the Hazara are a case of this).

The question of Britain is a bit more confused. Historians rely on textual evidence which points to Anglo-Saxon rule of Celtic-speaking populations in their kingdoms in the 7th and 8th century, in particular stipulations of different wergild (‘blood money’) for Saxons, noble and commoner, and Celts, noble and commoner. The existence of an elite Celtic speaking class suggests that Gildas’ allusions to genocide were exaggerations. Over the past 10 years a lot of exploration of the genetic variation within Britain has simply muddied the picture. Though some early Y chromosomal studies suggested sharp breaks between Wales and England, autosomal data don’t seem to show this. Rather, a reasonable model is that the Anglo-Saxons contributed a significant, but minority, element to England’s contribution. Their genetic impact drops as a decaying function of the distance from East Anglia, which was the heart of the “Saxon Shore,” but their cultural influence was not diluted along the wave of advance. This highlights the stark difference between genetic and cultural inheritance, the former is constrained in the nature of transmission in a way the latter is not. In fact, during the high tide of the Viking era in Britain’s history, the Saxon redoubt was Wessex, which genetic data show seem to has been minimally affected by German settlement. Rather, Wessex was likely conquered by the Saxonized.

Finally, what happened to multicultural Britain? The genetic data show a small effect, a random African lineage here and there which can not be explained by recent genealogy. An orders of magnitude less important than the Saxon migration. I think the reason is the simple that that urban areas were population sinks, and unless immigrants “went native” they disappeared into the genetic black hole. A reasonable historical analogy may be Lithuania. After the official union of the political structures of Lithuania and Poland in the 16th century the Lithuanian nobility was Polonized. The emergence of modern Lithuanian identity was to a great extent an elevation of Lithuanian peasant culture, which was left unaffected by Polonization. If extant literary or high cultural artifacts are used to reconstruct Lithuania’s history one might posit that Lithuanian’s disappeared in the early modern era, only to reemerge in the 19 century due to the ideology of nationalism.

There has long been a supposition that Latinization in Britain was relatively restricted and superficial compared to Gaul, where Celtic speech seems to have disappeared in the 5th century. This may be a inference made plausible by hindsight, because Britain was one region (the Balkans the other) where the ornaments of Roman high culture was totally extinguished in the face of barbarian invasions. By contrast, Gaul, Iberia and Italy all produced culturally hybrid elites who were Romanized. But from what I know the archaeological evidence does suggest a shift even among Romano-British warlords from a Roman to a British style in their material possessions over the 5th and 6th centuries (additionally, Roman commanders and legions stationed in Britain had a tendency to relocate to the continent in part because that was where the “action” was in terms of advancement and glory, so there may have been a sorting process whereby the most Romanized elites emigrated, while those who were willing to become barbarized, whether by going back to their Celtic roots, or becoming Saxonized, remained).

Here’s some gene related charts to support what I’m saying above about the muddle. On first inspection a Netherlandish affinity to many Briton’s is obvious (also, you can see it in Structure). Uniparental markers show the clines I’m alluding to above though, so where these samples come from within Britain matters a great deal at the scale we’re talking about. But the main problem is that some might argue that there have long been interactions between the low countries and southeast England because of their proximity, and not one particular Anglo-Saxon migration. Perhaps at some point it will be feasible to analyze the decay linkage disequilibrium (or see if there’s linkage disequilibrium) in southeast England to date the time of a putative admixture event. But of course the peoples of the North European Plain and those of England are relatively close genetically, so I’m not going to hold my breath. Ancient DNA will probably yield more sooner.